## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

Canonic TSS dynamics

Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.49)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.8)... Done.
## Bootstrap (r = 0.9)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  2:       1    ORF4 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  3:       1    ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  4:       1    ORF7 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  5:       1    ORF9 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  6:       1   ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  7:       1   ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  8:       1   ORF20 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  9:       1   ORF21 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10:       1   ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11:       1   ORF31 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12:       1   ORF34 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 13:       1   ORF38 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 14:       1   ORF50 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 15:       1   ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 16:       1   ORF56 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 17:       1   ORF61 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 18:       1   ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 19:       1  NOIR_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 20:       1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 21:       1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 22:       1   ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 23:       1  NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 24:       2    ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25:       2    ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26:       2    ORF8 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 27:       2   ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 28:       2   ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 29:       2   ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 30:       2   ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 31:       2   ORF22 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 32:       2   ORF23 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 33:       2   ORF24 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 34:       2   ORF25 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 35:       2   ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 36:       2   ORF27 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 37:       2   ORF28 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 38:       2   ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 39:       2   ORF32 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 40:       2   ORF33 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 41:       2 ORF35.5 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 42:       2   ORF36 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 43:       2   ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 44:       2   ORF39 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 45:       2     CTO 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 46:       2   ORF40 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 47:       2   ORF42 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 48:       2   ORF43 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 49:       2   ORF44 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 50:       2   ORF46 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 51:       2   ORF49 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 52:       2   ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 53:       2   ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 54:       2   ORF58 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 55:       2   ORF59 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 56:       2   ORF62 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 57:       2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 58:       2   ORF68 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 59:       2   ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 60:       2   ORF74 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 61:       2   ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 62:       3    ORF6 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 63:       3   ORF70 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 64:       4   ORF12 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 65:       4   ORF13 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 66:       4   ORF15 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 67:       4   ORF16 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 68:       4   ORF35 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 69:       4   ORF41 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 70:       4   ORF45 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 71:       4   ORF48 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 72:       4   ORF52 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 73:       4   ORF54 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 74:       4   ORF57 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 75:       4   ORF60 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 76:       4   ORF71 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 77:       4   ORF72 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 78:       5 ORF64_1 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 79:       5   ORF75 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c        pchi
##           <num>      <num>     <num>       <num>
##  1: 0.004367607 -1.8872285 0.9719524 0.032903167
##  2: 0.004367607 -1.8872285 0.9719524 0.032903167
##  3: 0.004367607 -1.8872285 0.9719524 0.032903167
##  4: 0.004367607 -1.8872285 0.9719524 0.032903167
##  5: 0.004367607 -1.8872285 0.9719524 0.032903167
##  6: 0.004367607 -1.8872285 0.9719524 0.032903167
##  7: 0.004367607 -1.8872285 0.9719524 0.032903167
##  8: 0.004367607 -1.8872285 0.9719524 0.032903167
##  9: 0.004367607 -1.8872285 0.9719524 0.032903167
## 10: 0.004367607 -1.8872285 0.9719524 0.032903167
## 11: 0.004367607 -1.8872285 0.9719524 0.032903167
## 12: 0.004367607 -1.8872285 0.9719524 0.032903167
## 13: 0.004367607 -1.8872285 0.9719524 0.032903167
## 14: 0.004367607 -1.8872285 0.9719524 0.032903167
## 15: 0.004367607 -1.8872285 0.9719524 0.032903167
## 16: 0.004367607 -1.8872285 0.9719524 0.032903167
## 17: 0.004367607 -1.8872285 0.9719524 0.032903167
## 18: 0.004367607 -1.8872285 0.9719524 0.032903167
## 19: 0.004367607 -1.8872285 0.9719524 0.032903167
## 20: 0.004367607 -1.8872285 0.9719524 0.032903167
## 21: 0.004367607 -1.8872285 0.9719524 0.032903167
## 22: 0.004367607 -1.8872285 0.9719524 0.032903167
## 23: 0.004367607 -1.8872285 0.9719524 0.032903167
## 24: 0.005032195 -1.1667586 0.7059510 0.008285088
## 25: 0.005032195 -1.1667586 0.7059510 0.008285088
## 26: 0.005032195 -1.1667586 0.7059510 0.008285088
## 27: 0.005032195 -1.1667586 0.7059510 0.008285088
## 28: 0.005032195 -1.1667586 0.7059510 0.008285088
## 29: 0.005032195 -1.1667586 0.7059510 0.008285088
## 30: 0.005032195 -1.1667586 0.7059510 0.008285088
## 31: 0.005032195 -1.1667586 0.7059510 0.008285088
## 32: 0.005032195 -1.1667586 0.7059510 0.008285088
## 33: 0.005032195 -1.1667586 0.7059510 0.008285088
## 34: 0.005032195 -1.1667586 0.7059510 0.008285088
## 35: 0.005032195 -1.1667586 0.7059510 0.008285088
## 36: 0.005032195 -1.1667586 0.7059510 0.008285088
## 37: 0.005032195 -1.1667586 0.7059510 0.008285088
## 38: 0.005032195 -1.1667586 0.7059510 0.008285088
## 39: 0.005032195 -1.1667586 0.7059510 0.008285088
## 40: 0.005032195 -1.1667586 0.7059510 0.008285088
## 41: 0.005032195 -1.1667586 0.7059510 0.008285088
## 42: 0.005032195 -1.1667586 0.7059510 0.008285088
## 43: 0.005032195 -1.1667586 0.7059510 0.008285088
## 44: 0.005032195 -1.1667586 0.7059510 0.008285088
## 45: 0.005032195 -1.1667586 0.7059510 0.008285088
## 46: 0.005032195 -1.1667586 0.7059510 0.008285088
## 47: 0.005032195 -1.1667586 0.7059510 0.008285088
## 48: 0.005032195 -1.1667586 0.7059510 0.008285088
## 49: 0.005032195 -1.1667586 0.7059510 0.008285088
## 50: 0.005032195 -1.1667586 0.7059510 0.008285088
## 51: 0.005032195 -1.1667586 0.7059510 0.008285088
## 52: 0.005032195 -1.1667586 0.7059510 0.008285088
## 53: 0.005032195 -1.1667586 0.7059510 0.008285088
## 54: 0.005032195 -1.1667586 0.7059510 0.008285088
## 55: 0.005032195 -1.1667586 0.7059510 0.008285088
## 56: 0.005032195 -1.1667586 0.7059510 0.008285088
## 57: 0.005032195 -1.1667586 0.7059510 0.008285088
## 58: 0.005032195 -1.1667586 0.7059510 0.008285088
## 59: 0.005032195 -1.1667586 0.7059510 0.008285088
## 60: 0.005032195 -1.1667586 0.7059510 0.008285088
## 61: 0.005032195 -1.1667586 0.7059510 0.008285088
## 62: 0.004900088 -1.7034767 1.0711351 0.077414527
## 63: 0.004900088 -1.7034767 1.0711351 0.077414527
## 64: 0.004859713 -1.8072219 1.1506135 0.987673767
## 65: 0.004859713 -1.8072219 1.1506135 0.987673767
## 66: 0.004859713 -1.8072219 1.1506135 0.987673767
## 67: 0.004859713 -1.8072219 1.1506135 0.987673767
## 68: 0.004859713 -1.8072219 1.1506135 0.987673767
## 69: 0.004859713 -1.8072219 1.1506135 0.987673767
## 70: 0.004859713 -1.8072219 1.1506135 0.987673767
## 71: 0.004859713 -1.8072219 1.1506135 0.987673767
## 72: 0.004859713 -1.8072219 1.1506135 0.987673767
## 73: 0.004859713 -1.8072219 1.1506135 0.987673767
## 74: 0.004859713 -1.8072219 1.1506135 0.987673767
## 75: 0.004859713 -1.8072219 1.1506135 0.987673767
## 76: 0.004859713 -1.8072219 1.1506135 0.987673767
## 77: 0.004859713 -1.8072219 1.1506135 0.987673767
## 78: 0.004602114 -0.4912168 1.1376079 0.445860724
## 79: 0.004602114 -0.4912168 1.1376079 0.445860724
##           se.bp          v         c        pchi

## [1] "ORF67_1" "ORF32"   "ORF58"   "ORF33"   "ORF35.5" "ORF25"   "ORF27"  
## [8] "ORF62"
## [1] 8
## [1] "ORF64_1" "ORF75"
## [1] 2

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  2:       1    ORF4 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  3:       1    ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  4:       1    ORF7 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  5:       1    ORF9 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  6:       1   ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  7:       1   ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  8:       1   ORF20 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  9:       1   ORF21 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10:       1   ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11:       1   ORF31 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12:       1   ORF34 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 13:       1   ORF38 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 14:       1   ORF50 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 15:       1   ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 16:       1   ORF56 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 17:       1   ORF61 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 18:       1   ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 19:       1  NOIR_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 20:       1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 21:       1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 22:       1   ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 23:       1  NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 24:       2    ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25:       2    ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26:       2   ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 27:       2   ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 28:       2   ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 29:       2   ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 30:       2   ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 31:       2   ORF28 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 32:       2   ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 33:       2   ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 34:       2   ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 35:       2   ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 36:       2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 37:       2   ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 38:       2   ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 39:       3    ORF6 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 40:       3   ORF70 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 41:       4    ORF8 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 42:       4   ORF22 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 43:       4   ORF23 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 44:       4   ORF24 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 45:       4   ORF25 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 46:       4   ORF27 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 47:       4   ORF32 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 48:       4   ORF33 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 49:       4 ORF35.5 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 50:       4   ORF36 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 51:       4   ORF39 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 52:       4     CTO 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 53:       4   ORF40 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 54:       4   ORF42 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 55:       4   ORF43 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 56:       4   ORF44 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 57:       4   ORF46 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 58:       4   ORF49 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 59:       4   ORF58 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 60:       4   ORF59 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 61:       4   ORF62 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 62:       4   ORF68 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 63:       4   ORF74 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 64:       5   ORF12 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 65:       5   ORF13 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 66:       5   ORF15 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 67:       5   ORF16 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 68:       5   ORF35 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 69:       5   ORF41 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 70:       5   ORF45 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 71:       5   ORF48 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 72:       5   ORF52 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 73:       5   ORF54 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 74:       5   ORF57 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 75:       5   ORF60 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 76:       5   ORF71 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 77:       5   ORF72 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 78:       6 ORF64_1 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 79:       6   ORF75 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c        pchi
##           <num>      <num>     <num>       <num>
##  1: 0.004367607 -1.8872285 0.9719524 0.032903167
##  2: 0.004367607 -1.8872285 0.9719524 0.032903167
##  3: 0.004367607 -1.8872285 0.9719524 0.032903167
##  4: 0.004367607 -1.8872285 0.9719524 0.032903167
##  5: 0.004367607 -1.8872285 0.9719524 0.032903167
##  6: 0.004367607 -1.8872285 0.9719524 0.032903167
##  7: 0.004367607 -1.8872285 0.9719524 0.032903167
##  8: 0.004367607 -1.8872285 0.9719524 0.032903167
##  9: 0.004367607 -1.8872285 0.9719524 0.032903167
## 10: 0.004367607 -1.8872285 0.9719524 0.032903167
## 11: 0.004367607 -1.8872285 0.9719524 0.032903167
## 12: 0.004367607 -1.8872285 0.9719524 0.032903167
## 13: 0.004367607 -1.8872285 0.9719524 0.032903167
## 14: 0.004367607 -1.8872285 0.9719524 0.032903167
## 15: 0.004367607 -1.8872285 0.9719524 0.032903167
## 16: 0.004367607 -1.8872285 0.9719524 0.032903167
## 17: 0.004367607 -1.8872285 0.9719524 0.032903167
## 18: 0.004367607 -1.8872285 0.9719524 0.032903167
## 19: 0.004367607 -1.8872285 0.9719524 0.032903167
## 20: 0.004367607 -1.8872285 0.9719524 0.032903167
## 21: 0.004367607 -1.8872285 0.9719524 0.032903167
## 22: 0.004367607 -1.8872285 0.9719524 0.032903167
## 23: 0.004367607 -1.8872285 0.9719524 0.032903167
## 24: 0.005032195 -1.1667586 0.7059510 0.008285088
## 25: 0.005032195 -1.1667586 0.7059510 0.008285088
## 26: 0.005032195 -1.1667586 0.7059510 0.008285088
## 27: 0.005032195 -1.1667586 0.7059510 0.008285088
## 28: 0.005032195 -1.1667586 0.7059510 0.008285088
## 29: 0.005032195 -1.1667586 0.7059510 0.008285088
## 30: 0.005032195 -1.1667586 0.7059510 0.008285088
## 31: 0.005032195 -1.1667586 0.7059510 0.008285088
## 32: 0.005032195 -1.1667586 0.7059510 0.008285088
## 33: 0.005032195 -1.1667586 0.7059510 0.008285088
## 34: 0.005032195 -1.1667586 0.7059510 0.008285088
## 35: 0.005032195 -1.1667586 0.7059510 0.008285088
## 36: 0.005032195 -1.1667586 0.7059510 0.008285088
## 37: 0.005032195 -1.1667586 0.7059510 0.008285088
## 38: 0.005032195 -1.1667586 0.7059510 0.008285088
## 39: 0.004900088 -1.7034767 1.0711351 0.077414527
## 40: 0.004900088 -1.7034767 1.0711351 0.077414527
## 41: 0.004859713 -1.8072219 1.1506135 0.987673767
## 42: 0.004859713 -1.8072219 1.1506135 0.987673767
## 43: 0.004859713 -1.8072219 1.1506135 0.987673767
## 44: 0.004859713 -1.8072219 1.1506135 0.987673767
## 45: 0.004859713 -1.8072219 1.1506135 0.987673767
## 46: 0.004859713 -1.8072219 1.1506135 0.987673767
## 47: 0.004859713 -1.8072219 1.1506135 0.987673767
## 48: 0.004859713 -1.8072219 1.1506135 0.987673767
## 49: 0.004859713 -1.8072219 1.1506135 0.987673767
## 50: 0.004859713 -1.8072219 1.1506135 0.987673767
## 51: 0.004859713 -1.8072219 1.1506135 0.987673767
## 52: 0.004859713 -1.8072219 1.1506135 0.987673767
## 53: 0.004859713 -1.8072219 1.1506135 0.987673767
## 54: 0.004859713 -1.8072219 1.1506135 0.987673767
## 55: 0.004859713 -1.8072219 1.1506135 0.987673767
## 56: 0.004859713 -1.8072219 1.1506135 0.987673767
## 57: 0.004859713 -1.8072219 1.1506135 0.987673767
## 58: 0.004859713 -1.8072219 1.1506135 0.987673767
## 59: 0.004859713 -1.8072219 1.1506135 0.987673767
## 60: 0.004859713 -1.8072219 1.1506135 0.987673767
## 61: 0.004859713 -1.8072219 1.1506135 0.987673767
## 62: 0.004859713 -1.8072219 1.1506135 0.987673767
## 63: 0.004859713 -1.8072219 1.1506135 0.987673767
## 64: 0.004602114 -0.4912168 1.1376079 0.445860724
## 65: 0.004602114 -0.4912168 1.1376079 0.445860724
## 66: 0.004602114 -0.4912168 1.1376079 0.445860724
## 67: 0.004602114 -0.4912168 1.1376079 0.445860724
## 68: 0.004602114 -0.4912168 1.1376079 0.445860724
## 69: 0.004602114 -0.4912168 1.1376079 0.445860724
## 70: 0.004602114 -0.4912168 1.1376079 0.445860724
## 71: 0.004602114 -0.4912168 1.1376079 0.445860724
## 72: 0.004602114 -0.4912168 1.1376079 0.445860724
## 73: 0.004602114 -0.4912168 1.1376079 0.445860724
## 74: 0.004602114 -0.4912168 1.1376079 0.445860724
## 75: 0.004602114 -0.4912168 1.1376079 0.445860724
## 76: 0.004602114 -0.4912168 1.1376079 0.445860724
## 77: 0.004602114 -0.4912168 1.1376079 0.445860724
## 78: 0.005252723 -1.2310691 0.9257357 0.181672372
## 79: 0.005252723 -1.2310691 0.9257357 0.181672372
##           se.bp          v         c        pchi

## [1] "ORF67_1" "ORF9"    "ORF73"   "ORF32"   "ORF62"   "ORF45"
## [1] 6
##  [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF45" "ORF48" "ORF52"
## [10] "ORF54" "ORF57" "ORF60" "ORF71" "ORF72"
## [1] 14

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  2:       1    ORF4 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  3:       1    ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  4:       1    ORF7 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  5:       1    ORF9 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  6:       1   ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  7:       1   ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  8:       1   ORF20 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  9:       1   ORF21 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10:       1   ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11:       1   ORF31 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12:       1   ORF34 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 13:       1   ORF38 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 14:       1   ORF50 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 15:       1   ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 16:       1   ORF56 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 17:       1   ORF61 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 18:       1   ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 19:       1  NOIR_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 20:       1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 21:       1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 22:       1   ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 23:       1  NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 24:       2    ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25:       2    ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26:       2   ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 27:       2   ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 28:       2   ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 29:       2   ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 30:       2   ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 31:       2   ORF28 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 32:       2   ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 33:       2   ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 34:       2   ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 35:       2   ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 36:       2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 37:       2   ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 38:       2   ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 39:       3    ORF6 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 40:       3   ORF70 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 41:       4    ORF8 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 42:       4   ORF22 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 43:       4   ORF23 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 44:       4   ORF24 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 45:       4   ORF25 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 46:       4   ORF27 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 47:       4   ORF32 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 48:       4   ORF33 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 49:       4 ORF35.5 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 50:       4   ORF36 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 51:       4   ORF39 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 52:       4     CTO 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 53:       4   ORF40 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 54:       4   ORF42 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 55:       4   ORF43 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 56:       4   ORF44 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 57:       4   ORF46 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 58:       4   ORF49 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 59:       4   ORF58 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 60:       4   ORF59 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 61:       4   ORF62 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 62:       4   ORF68 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 63:       4   ORF74 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 64:       5   ORF12 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 65:       5   ORF13 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 66:       5   ORF15 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 67:       5   ORF16 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 68:       5   ORF35 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 69:       5   ORF41 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 70:       5   ORF48 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 71:       5   ORF52 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 72:       5   ORF54 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 73:       5   ORF57 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 74:       5   ORF60 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 75:       5   ORF71 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 76:       5   ORF72 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 77:       6   ORF45 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 78:       7 ORF64_1 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 79:       7   ORF75 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c        pchi
##           <num>      <num>     <num>       <num>
##  1: 0.004367607 -1.8872285 0.9719524 0.032903167
##  2: 0.004367607 -1.8872285 0.9719524 0.032903167
##  3: 0.004367607 -1.8872285 0.9719524 0.032903167
##  4: 0.004367607 -1.8872285 0.9719524 0.032903167
##  5: 0.004367607 -1.8872285 0.9719524 0.032903167
##  6: 0.004367607 -1.8872285 0.9719524 0.032903167
##  7: 0.004367607 -1.8872285 0.9719524 0.032903167
##  8: 0.004367607 -1.8872285 0.9719524 0.032903167
##  9: 0.004367607 -1.8872285 0.9719524 0.032903167
## 10: 0.004367607 -1.8872285 0.9719524 0.032903167
## 11: 0.004367607 -1.8872285 0.9719524 0.032903167
## 12: 0.004367607 -1.8872285 0.9719524 0.032903167
## 13: 0.004367607 -1.8872285 0.9719524 0.032903167
## 14: 0.004367607 -1.8872285 0.9719524 0.032903167
## 15: 0.004367607 -1.8872285 0.9719524 0.032903167
## 16: 0.004367607 -1.8872285 0.9719524 0.032903167
## 17: 0.004367607 -1.8872285 0.9719524 0.032903167
## 18: 0.004367607 -1.8872285 0.9719524 0.032903167
## 19: 0.004367607 -1.8872285 0.9719524 0.032903167
## 20: 0.004367607 -1.8872285 0.9719524 0.032903167
## 21: 0.004367607 -1.8872285 0.9719524 0.032903167
## 22: 0.004367607 -1.8872285 0.9719524 0.032903167
## 23: 0.004367607 -1.8872285 0.9719524 0.032903167
## 24: 0.005032195 -1.1667586 0.7059510 0.008285088
## 25: 0.005032195 -1.1667586 0.7059510 0.008285088
## 26: 0.005032195 -1.1667586 0.7059510 0.008285088
## 27: 0.005032195 -1.1667586 0.7059510 0.008285088
## 28: 0.005032195 -1.1667586 0.7059510 0.008285088
## 29: 0.005032195 -1.1667586 0.7059510 0.008285088
## 30: 0.005032195 -1.1667586 0.7059510 0.008285088
## 31: 0.005032195 -1.1667586 0.7059510 0.008285088
## 32: 0.005032195 -1.1667586 0.7059510 0.008285088
## 33: 0.005032195 -1.1667586 0.7059510 0.008285088
## 34: 0.005032195 -1.1667586 0.7059510 0.008285088
## 35: 0.005032195 -1.1667586 0.7059510 0.008285088
## 36: 0.005032195 -1.1667586 0.7059510 0.008285088
## 37: 0.005032195 -1.1667586 0.7059510 0.008285088
## 38: 0.005032195 -1.1667586 0.7059510 0.008285088
## 39: 0.004900088 -1.7034767 1.0711351 0.077414527
## 40: 0.004900088 -1.7034767 1.0711351 0.077414527
## 41: 0.004859713 -1.8072219 1.1506135 0.987673767
## 42: 0.004859713 -1.8072219 1.1506135 0.987673767
## 43: 0.004859713 -1.8072219 1.1506135 0.987673767
## 44: 0.004859713 -1.8072219 1.1506135 0.987673767
## 45: 0.004859713 -1.8072219 1.1506135 0.987673767
## 46: 0.004859713 -1.8072219 1.1506135 0.987673767
## 47: 0.004859713 -1.8072219 1.1506135 0.987673767
## 48: 0.004859713 -1.8072219 1.1506135 0.987673767
## 49: 0.004859713 -1.8072219 1.1506135 0.987673767
## 50: 0.004859713 -1.8072219 1.1506135 0.987673767
## 51: 0.004859713 -1.8072219 1.1506135 0.987673767
## 52: 0.004859713 -1.8072219 1.1506135 0.987673767
## 53: 0.004859713 -1.8072219 1.1506135 0.987673767
## 54: 0.004859713 -1.8072219 1.1506135 0.987673767
## 55: 0.004859713 -1.8072219 1.1506135 0.987673767
## 56: 0.004859713 -1.8072219 1.1506135 0.987673767
## 57: 0.004859713 -1.8072219 1.1506135 0.987673767
## 58: 0.004859713 -1.8072219 1.1506135 0.987673767
## 59: 0.004859713 -1.8072219 1.1506135 0.987673767
## 60: 0.004859713 -1.8072219 1.1506135 0.987673767
## 61: 0.004859713 -1.8072219 1.1506135 0.987673767
## 62: 0.004859713 -1.8072219 1.1506135 0.987673767
## 63: 0.004859713 -1.8072219 1.1506135 0.987673767
## 64: 0.004602114 -0.4912168 1.1376079 0.445860724
## 65: 0.004602114 -0.4912168 1.1376079 0.445860724
## 66: 0.004602114 -0.4912168 1.1376079 0.445860724
## 67: 0.004602114 -0.4912168 1.1376079 0.445860724
## 68: 0.004602114 -0.4912168 1.1376079 0.445860724
## 69: 0.004602114 -0.4912168 1.1376079 0.445860724
## 70: 0.004602114 -0.4912168 1.1376079 0.445860724
## 71: 0.004602114 -0.4912168 1.1376079 0.445860724
## 72: 0.004602114 -0.4912168 1.1376079 0.445860724
## 73: 0.004602114 -0.4912168 1.1376079 0.445860724
## 74: 0.004602114 -0.4912168 1.1376079 0.445860724
## 75: 0.004602114 -0.4912168 1.1376079 0.445860724
## 76: 0.004602114 -0.4912168 1.1376079 0.445860724
## 77: 0.005252723 -1.2310691 0.9257357 0.181672372
## 78: 0.004974133 -1.5296004 0.9769568 0.424389515
## 79: 0.004974133 -1.5296004 0.9769568 0.424389515
##           se.bp          v         c        pchi

## [1] "ORF67_1" "ORF9"    "ORF73"   "ORF27"   "ORF32"   "ORF62"
## [1] 6
##  [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF48" "ORF52" "ORF54"
## [10] "ORF57" "ORF60" "ORF71" "ORF72"
## [1] 13

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  2:       1    ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  3:       1   ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  4:       1   ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  5:       1   ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  6:       1   ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  7:       1   ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  8:       1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  9:       1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10:       1   ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11:       1  NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12:       2    ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 13:       2    ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 14:       2   ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 15:       2   ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 16:       2   ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 17:       2   ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 18:       2   ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 19:       2   ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 20:       2   ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 21:       2   ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 22:       2   ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 23:       2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 24:       2   ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25:       2   ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26:       3    ORF4 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 27:       3    ORF7 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 28:       3    ORF9 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 29:       3   ORF20 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 30:       3   ORF21 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 31:       3   ORF31 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 32:       3   ORF34 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 33:       3   ORF38 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 34:       3   ORF50 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 35:       3   ORF56 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 36:       3   ORF61 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 37:       3  NOIR_1 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 38:       4    ORF6 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 39:       4   ORF70 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 40:       5    ORF8 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 41:       5   ORF22 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 42:       5   ORF23 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 43:       5   ORF24 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 44:       5   ORF25 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 45:       5   ORF33 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 46:       5 ORF35.5 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 47:       5   ORF36 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 48:       5   ORF39 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 49:       5     CTO 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 50:       5   ORF40 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 51:       5   ORF42 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 52:       5   ORF43 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 53:       5   ORF44 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 54:       5   ORF46 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 55:       5   ORF49 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 56:       5   ORF58 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 57:       5   ORF62 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 58:       5   ORF68 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 59:       5   ORF74 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 60:       6   ORF12 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 61:       6   ORF13 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 62:       6   ORF15 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 63:       6   ORF16 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 64:       6   ORF35 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 65:       6   ORF41 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 66:       6   ORF48 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 67:       6   ORF52 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 68:       6   ORF54 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 69:       6   ORF57 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 70:       6   ORF60 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 71:       6   ORF71 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 72:       6   ORF72 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 73:       7   ORF27 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 74:       7   ORF32 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 75:       7   ORF59 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 76:       8   ORF28 0.8210270 0.9735951 0.4373670 0.022875031 0.0049505146
## 77:       9   ORF45 0.5651379 0.9248487 0.3271761 0.043440538 0.0119522826
## 78:      10 ORF64_1 0.9824929 0.9988394 0.5150579 0.003567073 0.0003270244
## 79:      10   ORF75 0.9824929 0.9988394 0.5150579 0.003567073 0.0003270244
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c         pchi
##           <num>      <num>     <num>        <num>
##  1: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  2: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  3: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  4: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  5: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  6: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  7: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  8: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  9: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 10: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 11: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 12: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 13: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 14: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 15: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 16: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 17: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 18: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 19: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 20: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 21: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 22: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 23: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 24: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 25: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 26: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 27: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 28: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 29: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 30: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 31: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 32: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 33: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 34: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 35: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 36: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 37: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 38: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 39: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 40: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 41: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 42: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 43: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 44: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 45: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 46: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 47: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 48: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 49: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 50: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 51: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 52: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 53: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 54: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 55: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 56: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 57: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 58: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 59: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 60: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 61: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 62: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 63: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 64: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 65: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 66: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 67: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 68: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 69: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 70: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 71: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 72: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 73: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 74: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 75: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 76: 0.005277089 -0.8894121 1.0470603 0.0007092392
## 77: 0.004937236 -0.4953695 0.9430937 0.2285253818
## 78: 0.005407688 -1.5417408 1.5039873 0.6383969620
## 79: 0.005407688 -1.5417408 1.5039873 0.6383969620
##           se.bp          v         c         pchi

## [1] "ORF55" "ORF73" "ORF62" "ORF27" "ORF32" "ORF59"
## [1] 6
##  [1] "ORF8"    "ORF22"   "ORF23"   "ORF24"   "ORF25"   "ORF33"   "ORF35.5"
##  [8] "ORF36"   "ORF39"   "CTO"     "ORF40"   "ORF42"   "ORF43"   "ORF44"  
## [15] "ORF46"   "ORF49"   "ORF58"   "ORF62"   "ORF68"   "ORF74"   "ORF45"
## [1] 21

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  2:       1    ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  3:       1   ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  4:       1   ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  5:       1   ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  6:       1   ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  7:       1   ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  8:       1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  9:       1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10:       1   ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11:       1  NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12:       2    ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 13:       2    ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 14:       2   ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 15:       2   ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 16:       2   ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 17:       2   ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 18:       2   ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 19:       2   ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 20:       2   ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 21:       2   ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 22:       2   ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 23:       2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 24:       2   ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25:       2   ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26:       3    ORF4 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 27:       3    ORF9 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 28:       3   ORF20 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 29:       3   ORF21 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 30:       3   ORF31 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 31:       3   ORF34 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 32:       3   ORF38 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 33:       3   ORF50 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 34:       3   ORF61 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 35:       4    ORF6 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 36:       4   ORF70 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 37:       5    ORF7 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 38:       5   ORF56 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 39:       5  NOIR_1 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 40:       6    ORF8 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 41:       6   ORF22 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 42:       6   ORF23 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 43:       6   ORF24 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 44:       6   ORF25 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 45:       6   ORF33 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 46:       6 ORF35.5 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 47:       6   ORF36 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 48:       6   ORF39 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 49:       6     CTO 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 50:       6   ORF40 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 51:       6   ORF42 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 52:       6   ORF43 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 53:       6   ORF44 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 54:       6   ORF46 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 55:       6   ORF49 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 56:       6   ORF58 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 57:       6   ORF62 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 58:       6   ORF68 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 59:       6   ORF74 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 60:       7   ORF12 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 61:       7   ORF13 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 62:       7   ORF15 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 63:       7   ORF16 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 64:       7   ORF35 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 65:       7   ORF41 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 66:       7   ORF48 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 67:       7   ORF52 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 68:       7   ORF54 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 69:       7   ORF57 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 70:       7   ORF60 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 71:       7   ORF71 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 72:       7   ORF72 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 73:       8   ORF27 0.8210270 0.9735951 0.4373670 0.022875031 0.0049505146
## 74:       8   ORF59 0.8210270 0.9735951 0.4373670 0.022875031 0.0049505146
## 75:       9   ORF28 0.5651379 0.9248487 0.3271761 0.043440538 0.0119522826
## 76:      10   ORF32 0.9824929 0.9988394 0.5150579 0.003567073 0.0003270244
## 77:      11   ORF45 0.7492275 0.9767156 0.2557177 0.034782397 0.0050850400
## 78:      12 ORF64_1 0.5275231 0.9246028 0.2892245 0.047108368 0.0121954635
## 79:      12   ORF75 0.5275231 0.9246028 0.2892245 0.047108368 0.0121954635
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c         pchi
##           <num>      <num>     <num>        <num>
##  1: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  2: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  3: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  4: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  5: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  6: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  7: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  8: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  9: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 10: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 11: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 12: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 13: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 14: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 15: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 16: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 17: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 18: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 19: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 20: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 21: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 22: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 23: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 24: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 25: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 26: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 27: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 28: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 29: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 30: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 31: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 32: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 33: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 34: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 35: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 36: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 37: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 38: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 39: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 40: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 41: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 42: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 43: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 44: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 45: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 46: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 47: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 48: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 49: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 50: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 51: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 52: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 53: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 54: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 55: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 56: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 57: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 58: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 59: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 60: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 61: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 62: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 63: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 64: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 65: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 66: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 67: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 68: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 69: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 70: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 71: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 72: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 73: 0.005277089 -0.8894121 1.0470603 0.0007092392
## 74: 0.005277089 -0.8894121 1.0470603 0.0007092392
## 75: 0.004937236 -0.4953695 0.9430937 0.2285253818
## 76: 0.005407688 -1.5417408 1.5039873 0.6383969620
## 77: 0.004595546 -0.6667982 1.3234023 0.9043442194
## 78: 0.004767205 -0.4405398 0.9961916 0.2426264521
## 79: 0.004767205 -0.4405398 0.9961916 0.2426264521
##           se.bp          v         c         pchi

## [1] "NOIR_2" "ORF1"   "ORF55"  "ORF73"  "ORF62"
## [1] 5
## [1] "ORF7"    "ORF56"   "NOIR_1"  "ORF28"   "ORF64_1" "ORF75"
## [1] 6

Selected number of clusters: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  2:       1    ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  3:       1   ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  4:       1   ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  5:       1   ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  6:       1   ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  7:       1   ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  8:       1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
##  9:       1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10:       1   ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11:       1  NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12:       2    ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 13:       2    ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 14:       2   ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 15:       2   ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 16:       2   ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 17:       2   ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 18:       2   ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 19:       2   ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 20:       2   ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 21:       2   ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 22:       2   ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 23:       2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 24:       2   ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25:       2   ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26:       3    ORF4 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 27:       3    ORF9 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 28:       3   ORF20 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 29:       3   ORF21 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 30:       3   ORF31 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 31:       3   ORF34 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 32:       3   ORF38 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 33:       3   ORF50 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 34:       3   ORF61 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 35:       4    ORF6 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 36:       4   ORF70 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 37:       5    ORF7 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 38:       5   ORF56 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 39:       5  NOIR_1 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 40:       6    ORF8 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 41:       6   ORF22 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 42:       6   ORF23 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 43:       6   ORF24 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 44:       6   ORF25 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 45:       6   ORF33 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 46:       6 ORF35.5 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 47:       6   ORF36 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 48:       6   ORF39 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 49:       6     CTO 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 50:       6   ORF40 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 51:       6   ORF42 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 52:       6   ORF43 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 53:       6   ORF44 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 54:       6   ORF46 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 55:       6   ORF49 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 56:       6   ORF58 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 57:       6   ORF62 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 58:       6   ORF68 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 59:       6   ORF74 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 60:       7   ORF12 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 61:       7   ORF13 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 62:       7   ORF15 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 63:       7   ORF16 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 64:       7   ORF35 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 65:       7   ORF41 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 66:       7   ORF48 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 67:       7   ORF52 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 68:       7   ORF54 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 69:       7   ORF57 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 70:       7   ORF60 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 71:       7   ORF71 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 72:       7   ORF72 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 73:       8   ORF27 0.8210270 0.9735951 0.4373670 0.022875031 0.0049505146
## 74:       8   ORF59 0.8210270 0.9735951 0.4373670 0.022875031 0.0049505146
## 75:       9   ORF28 0.5651379 0.9248487 0.3271761 0.043440538 0.0119522826
## 76:      10   ORF32 0.9824929 0.9988394 0.5150579 0.003567073 0.0003270244
## 77:      11   ORF45 0.7492275 0.9767156 0.2557177 0.034782397 0.0050850400
## 78:      12 ORF64_1 0.5275231 0.9246028 0.2892245 0.047108368 0.0121954635
## 79:      12   ORF75 0.5275231 0.9246028 0.2892245 0.047108368 0.0121954635
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c         pchi
##           <num>      <num>     <num>        <num>
##  1: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  2: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  3: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  4: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  5: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  6: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  7: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  8: 0.004367607 -1.8872285 0.9719524 0.0329031670
##  9: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 10: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 11: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 12: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 13: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 14: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 15: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 16: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 17: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 18: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 19: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 20: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 21: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 22: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 23: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 24: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 25: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 26: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 27: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 28: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 29: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 30: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 31: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 32: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 33: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 34: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 35: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 36: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 37: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 38: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 39: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 40: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 41: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 42: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 43: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 44: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 45: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 46: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 47: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 48: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 49: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 50: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 51: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 52: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 53: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 54: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 55: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 56: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 57: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 58: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 59: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 60: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 61: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 62: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 63: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 64: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 65: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 66: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 67: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 68: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 69: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 70: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 71: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 72: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 73: 0.005277089 -0.8894121 1.0470603 0.0007092392
## 74: 0.005277089 -0.8894121 1.0470603 0.0007092392
## 75: 0.004937236 -0.4953695 0.9430937 0.2285253818
## 76: 0.005407688 -1.5417408 1.5039873 0.6383969620
## 77: 0.004595546 -0.6667982 1.3234023 0.9043442194
## 78: 0.004767205 -0.4405398 0.9961916 0.2426264521
## 79: 0.004767205 -0.4405398 0.9961916 0.2426264521
##           se.bp          v         c         pchi

## [1] "NOIR_2" "ORF1"   "ORF55"  "ORF73"  "ORF62"
## [1] 5
## [1] "ORF7"    "ORF56"   "NOIR_1"  "ORF28"   "ORF64_1" "ORF75"
## [1] 6

Remove genes from clusters ?

## [1] "ORF7"    "ORF56"   "NOIR_1"  "ORF28"   "ORF64_1" "ORF75"
## [1] 6
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       6    20
##  2:       2    14
##  3:       7    13
##  4:       1    11
##  5:       3     9
##  6:       5     3
##  7:       4     2
##  8:       8     2
##  9:      12     2
## 10:       9     1
## 11:      10     1
## 12:      11     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters